DNA manufacturing, storage, and access system

ABSTRACT

A system includes a synthesizer unit having a fluid input to receive fluids and a communication input to receive commands to synthesize data-encoded DNA sequences and cleave the DNA. A first flexible chemistry reaction chamber module may be fluidically coupled to the synthesizer unit to receive the data-encoded DNA sequences and amplify the sequences. A deposition unit may be fluidically coupled to the first flexible chemistry reaction chamber module to receive the amplified DNA sequences and encapsulate the amplified DNA sequences into one or more wells in a storage plate for storage and retrieval to and from a plate storage unit. Retrieved DNA may be processed and read by further units.

BACKGROUND

Current storage technologies can no longer keep pace with exponentiallygrowing amounts of data. Synthetic DNA offers an attractive alternativedue to its potential information density of ˜10¹⁸ B/mm³, 10⁷ timesdenser than magnetic tape, and potential durability of thousands ofyears. Recent advances in DNA data storage have highlighted technicalchallenges, in particular, with coding and random access, but havestored only modest amounts of data in synthetic DNA.

SUMMARY

A system includes a synthesizer unit having a fluid input to receivefluids and a communication input to receive commands to synthesizedata-encoded DNA sequences and cleave the DNA. A first flexiblechemistry reaction chamber module may be fluidically coupled to thesynthesizer unit to receive the data-encoded DNA sequences and amplifythe sequences. A deposition unit may be fluidically coupled to the firstflexible chemistry reaction chamber module to receive the amplified DNAsequences and encapsulate the amplified DNA sequences into one or morewells in a storage plate for storage and retrieval to and from a platestorage unit.

A method includes synthesizing data-encoded DNA sequences and cleavingthe DNA sequences via a synthesizer unit having a fluid input to receivefluids and a communication input to receive commands to synthesizedata-encoded sequences and cleave the DNA, amplifying the DNA sequencesvia a first flexible chemistry reaction chamber module fluidicallycoupled to the synthesizer unit, and receiving the amplified DNAsequences and encapsulating the amplified DNA sequences via a depositionunit fluidically coupled to the first flexible chemistry reactionchamber module into one or more wells in a storage plate for storage andretrieval to and from a plate storage unit.

A machine-readable storage device has instructions for execution by aprocessor of the machine to perform operations. The operations includecontrolling synthesizing data-encoded DNA sequences and cleaving the DNAsequences via a synthesizer unit having a fluid input to receive fluidsand a communication input to receive commands to synthesize data-encodedsequences and cleave the DNA, controlling amplifying the DNA sequencesvia a first flexible chemistry reaction chamber module fluidicallycoupled to the synthesizer unit, and controlling receiving of theamplified DNA sequences and encapsulating the amplified DNA sequencesvia a deposition unit fluidically coupled to the first flexiblechemistry reaction chamber module into one or more wells in a storageplate for storage and retrieval to and from a plate storage unit.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1A is a block pictorial flow diagram of a data-encoded DNAmanufacturing, storage, and access system according to an exampleembodiment.

FIG. 1B is a block diagram illustrating the components of FIG. 1A,showing their connections via fluidics and robotic mechanisms fortransferring DNA between the components according to an exampleembodiment.

FIG. 2 is a flowchart illustration of a method for controlling thecomponents shown in FIGS. 1A and 1B according to an example embodiment.

FIG. 3 is a block perspective view of a wafer for use in synthesizingand sequencing data-encoded DNA according to an example embodiment.

FIG. 4A is a perspective view of a synthesis module unit according to anexample embodiment.

FIG. 4B is a cut-away perspective view of the synthesis module unitaccording to an example embodiment.

FIG. 5 is a block cross section of a flexible chemistry reaction chambermodule unit for amplifying data-encoded DNA according to an exampleembodiment.

FIGS. 6A, 6B, and 6C are block cross sections of the flexible chemistryreaction chamber module illustrating different positions of layersduring data-encoded DNA processing creating different flexible chemistryreaction chamber module states according to an example embodiment.

FIG. 7 is a perspective illustration of devices involved in depositingthe DNA according to an example embodiment.

FIG. 8 is a partial perspective representation of a storage plate havingan array of wells or spots according to an example embodiment.

FIG. 9A is a block perspective view of a storage library with a storageplate positioned proximate a slot according to an example embodiment.

FIG. 9B is a perspective view illustrating a storage plate partiallyinserted into a slot of a storage library according to an exampleembodiment.

FIG. 9C is a perspective view of a storage plate according to an exampleembodiment.

FIG. 9D is a perspective view of a back of the storage library accordingto an example embodiment.

FIG. 9E is a perspective view of a robot arm protrusion according to anexample embodiment.

FIG. 10 is a block perspective view of a plunger removing a capsule ofDNA from a storage plate well according to an example embodiment.

FIG. 11A is a block cross section of a rehydration unit according to anexample embodiment.

FIG. 11B is a semi-transparent perspective view of a combined reactionchamber and rehydration module according to an example embodiment.

FIG. 12 is a block perspective and exploded block perspective view of asequencing module according to an example embodiment.

FIG. 13 is a block schematic diagram of a computer system to implementone or more methods and control devices according to exampleembodiments.

FIG. 14 is a perspective view of a system for processing a plurality ofwafers held in a wafer boat according to an example embodiment.

FIG. 15 is a perspective view of a device for processing one or morestacks of wafers according to an example embodiment.

DETAILED DESCRIPTION

In the following description, reference is made to the accompanyingdrawings that form a part hereof, and in which is shown by way ofillustration specific embodiments which may be practiced. Theseembodiments are described in sufficient detail to enable those skilledin the art to practice the inventive subject matter, and it is to beunderstood that other embodiments may be utilized and that structural,logical and electrical changes may be made without departing from thescope of the present inventive subject matter. The following descriptionof example embodiments is, therefore, not to be taken in a limitedsense, and the scope of the present inventive subject matter is definedby the appended claims.

The functions or algorithms described herein may be implemented insoftware in one embodiment. The software may consist ofcomputer-executable instructions stored on computer-readable media orcomputer-readable storage device such as one or more non-transitorymemories or other type of hardware based storage devices, either localor networked. Further, such functions correspond to modules, which maybe software, hardware, firmware or any combination thereof. Multiplefunctions may be performed in one or more modules as desired, and theembodiments described are merely examples. The software may be executedon a digital signal processor, ASIC, microprocessor, or other type ofprocessor operating on a computer system, such as a personal computer,server or other computer system, turning such computer system into aspecifically programmed machine. The term “module” is also used hereinto refer to various mechanical devices, systems, and units forsynthesizing, processing, and sequencing DNA.

The functionality can be configured to perform an operation using, forinstance, software, hardware, firmware, or the like. For example, thephrase “configured to” can refer to a logic circuit structure of ahardware element that is to implement the associated functionality. Thephrase “configured to” may also refer to structural modifications ofphysical components to accomplish a stated function. The phrase“configured to” can also refer to a logic circuit structure of ahardware element that is designed to implement the coding design ofassociated functionality of firmware or software.

Furthermore, methods for controlling various devices and mechanicalcomponents, such as robots, microfluidic tubes and valves, actuators andthe like, may be implemented as a method, apparatus, or article ofmanufacture using standard programming and engineering techniques toproduce software, firmware, hardware, or any combination thereof tocontrol a computing device to implement the methods. The term “articleof manufacture,” as used herein, is intended to encompass a computerprogram accessible from any computer-readable storage device or media.Computer-readable storage media can include, but are not limited to,magnetic storage devices, e.g., hard disk, floppy disk, magnetic strips,optical disk, compact disk (CD), digital versatile disk (DVD), smartcards, flash memory devices, among others. In contrast,computer-readable media. i.e., not storage media, may additionallyinclude communication media such as transmission media for wirelesssignals and the like.

Recent advances in DNA data storage have highlighted technicalchallenges, in particular, coding and random access, but have storedonly modest amounts of data in synthetic DNA.

High throughput synthesis and sequencing of DNA results in immersing DNAinto fluids, exposing the DNA to light, moving batches of DNA around,etc. The term “fluids,” as used herein, refers to liquids used invarious DNA processes, including at least DNA synthesis, amplification,preparation for sequencing, and sequencing. Creating an entirely newsystem to perform these tasks, yet protect associated electronics, maybe expensive. Various embodiments of the present inventive subjectmatter reuse equipment, pipelines, and automation developed forsemiconductor fabrication for these purposes, and may also utilize newlydesigned equipment.

DNA synthesis consists of exposing a surface to sequential chemicalbaths. In various embodiments, the surface may be formed of glass orsilicon, silica coatings, silicon dioxide, aluminum oxide, silicacoatings, titanium oxide, other metal oxides, metal nitrides, grapheneand graphites, or various organic polymer coatings. The surface can besolid, porous, or with various patterned topographies. The surface maybe patterned following commonly used semiconductor processing, and mayalso be functionalized for DNA synthesis. Synthesis may also includeactivating electronics on the surface, shining light selectively onparts of the surface, or depositing selectively on parts of the surface.In various embodiments, such synthesis steps may be done using siliconfabrication equipment in a fab-like pipeline.

Sequencing also utilizes operations similar to synthesis and may includethe use of cameras to capture optical features on the DNA attached tothe surface, or the use of nanopores or other electrical sequencingtechnology that benefits from the bulk fluidics provided by thesemiconductor fabrication equipment.

In some embodiments, wafer-shaped substrates are used for both synthesisand sequencing of DNA in a DNA synthesis/sequencing unit. Chips, wafers,synthesis surfaces, and sequencing surfaces may be brought to fluids andother equipment that operates over the DNA. Automation equipment may usedevices such as wafer boats to move chips/wafers and fluidics(microfluidics, microfluidics, tubes, etc.) to transfer DNA betweenequipment. Much of the same equipment used in semiconductor fabrication,such as lithography, equipment to expose to chemicals in batch, testingequipment to drive electronics in chips/wafers, and other equipment,along with newly designed devices for processing DNA, may be used invarious embodiments.

Large-scale DNA manufacturing is challenging due to the level ofautomation and delivery/removal of chemical reagents to surfaces wherethe DNA is grown. In one embodiment, a rotatable stacked assembly ofwafers for DNA synthesis is mounted on an axis in a chamber of a DNAsynthesis module or unit. Stacking of the wafers provides an increasedsurface area per volume for processing DNA. Rotation of the stack aboutthe axis aids in centrifuging reagents out of the space between thewafers. Pressurization of the chamber or connecting the chamber to avacuum source further assists with complete removal of used reagents andaddition of new reagents in the chamber.

The wafers where the DNA grows may be mounted on a stack. The stack ismounted on an axis. If wafers need to communicate with the exterior(optical control, pH-based electronic control, and mechanical throttlingcontrol solutions), the wafers are connected via flat flex circuits,wirelessly via transceivers, or another connector. The wafers may beplanar or have spacers to separate the wafers, give the stack morerigidity, and/or reduce the empty/reagent space in the chamber.

For DNA synthesis, the wafers may be exposed to reagents in series,interspersed with activation of elements on the wafers (light sourcesfor optical control, electrodes for pH-based measurements or thermalcontrol, and throttles for mechanical control). The reagent delivery andremoval is challenging for a stack of wafers.

By enclosing the stack of wafers in a chamber and connecting the chamberto a pressure control source, fast delivery and removal of reagent isprovided. First, the chamber is emptied by spinning the wafers andapplying a positive pressure via an inert gas to overcome a pressuregradient caused by the spinning. Once emptied, a valve is opened thatlets the selected reagent in, completely filling the empty spaces in thechamber. Negative pressure in the chamber may be used to facilitatefilling. Next, if needed, active elements in the chip are activated.Finally, spinning and positive pressure may be used again to remove thereagent from the chamber, leaving it ready for the next step/reagent.

Cleavage and deprotection of the DNA may also be performed stepwise orsimultaneously in the chamber, either via pressurized gas injection, ora solution that is then heated, or a combination of pressurized gasinjection and heating. Cleavage may be performed via one or more methodsincluding acid, base, oxidative, reductive, thermal, photolytic,electrochemical or enzymatic cleavage methods. The selection of reagentsentering and exiting the chamber may be done via a configurable valvesystem.

The use of DNA for data storage and other applications involves DNAcapture by solid phase extraction or membrane filtration methods,filtration, size selection, mixing with other reagents, temperaturecycling, and agitation. Various embodiments described herein may be usedto fully automate such use. A DNA capture and elution system may becoupled with a flexible chemistry reaction chamber module having achamber that can be opened/closed, heated/cooled, and agitatedautomatically.

Some automated solutions use magnetic bead extraction for DNA separationand pipettes for moving DNA solutions around test tubes. In oneembodiment, a flexible chemistry reaction chamber module consists of aDNA capture and DNA release at a respective inlet and outlet of achamber. A top plate and a bottom plate slide to open and close thechamber at appropriate times. The fluids may move in and out by gravityor due to pressurization of the incoming and outgoing tubing connectedto the flexible chemistry reaction chamber module. In one embodiment,the DNA may be bound to magnetic or other kind of beads.

One use for the flexible chemistry reaction chamber module includes DNAsize selection and polymerase chain reaction (PCR) amplification thatmay be performed after the DNA is synthesized by the DNA synthesis unit.Initially, the top and bottom of the unit are in the open position. Afluid carrying DNA coming from the DNA synthesis unit passes through theopenings and is potentially recirculated. In the process, DNA iscaptured in the chamber by solid phase extraction or membrane filtrationmethods and the remaining material flows away into a waste or reagentrecycling unit. The capturing mechanism may be part of the filter, ordisposed to be exposed to DNA in or from the chamber. Next, the bottomis closed, and the DNA is eluted with a different fluid. Other reagentsare added to prepare the contents for PCR. The top is closed and PCR isperformed by temperature-cycling implemented by the heating/coolingsystem. Once complete, the bottom is opened, and the fluid passesthrough the second capture system (again, potentially recirculated tomaximize capture). Finally, the DNA is eluted with a different fluid. Insome embodiments, an additional opening may be provided for receivingstored capsules of DNA for rehydrating and otherwise processing the DNA.

Storage of DNA for long periods of time requires a system to preserve,organize, and densely pack large quantities of DNA in a small volume.Various embodiments meet these requirements and allow for automation ofoperations, namely, encapsulation, storage, retrieval, and recovery ofthe DNA.

In one embodiment, a set of slides or plates containing an array ofspots, cavities, or wells (all referred to herein as wells) forpreserving the DNA may be used. These plates are collectively stored ina storage container as “drawers” that slide in for storage and out forretrieval. Each plate may have features to facilitate capturing andmovement by a robot, and may also be identified with a unique visualfeature like a 1D or 2D barcode or other (e.g., text or numbers).Metadata about what is stored and the location of the data-encoded DNAin the storage container may be recorded by a file system or database.

After it is synthesized, extracted, and/or amplified, the DNA is readyto be stored. The DNA may be stored in a single spot, cavity, or well,or aliquoted into multiple wells, either on the same plate, or differentplates. DNA may also be added to existing, partially filled wells.

The cavities or wells are configured to capture the DNA and let thesolvent flow out. This is accomplished either by a membrane at thebottom (or middle, or anywhere else in the cavity) that captures theDNA, or by a different porous solid that fills the cavity and capturesthe DNA in its pores. DNA capture may also be facilitated by the use ofelectrostatic forces. Magnetic force may be used to capture DNA providedthe DNA was bound to a magnetic bead in a prior step. Reagents may beadded one or more times to make the DNA adhere to the beads. Once theDNA is captured in a well, more chemicals may be added to help preservethe DNA. If needed, the contents are dried and then the well may behermetically sealed with a solid film, membrane, or other material, withinert gas included within the well with the dried contents. In furtherembodiments, wells may be individually sealed with local well-coveringfilms, membranes, or other materials. Once the DNA is stored, the platemay be placed by a robot in the larger container for storage. A platemay not be entirely filled at once. Plates can be moved in and out ofthe large container in a reversible manner.

When it is time to recover the DNA, the location is determined by thefile system or database from the metadata, and a robot retrieves theplate. The visual feature may also be used to identify a desired plate.The desired DNA is removed from the plate like a “blister package”,there a rod-like plunger pushes the material out of the cavity and intoanother container that is used for de-encapsulation (e.g., chemicalreaction chamber in the flexible chemistry reaction chamber module). Ina further embodiment, a microfluidic board may be used to re-dissolvethe DNA in a spot.

A rehydration unit, similar to a flexible chemistry reaction chambermodule, may be used for de-encapsulation of retrieved stored DNA. Aftera blister of encapsulated DNA is dropped through a different or the sameopening into the rehydration unit chamber, other reagents are added forde-encapsulation and rehydration. These reagents may be drained orrecirculated using the same method as above (opening/closinginlet/outlet modules and using the capture system to hold the DNA inplace). The de-encapsulated DNA may then be amplified via a flexiblechemistry reaction chamber module similar to or the same as the abovedescribed flexible chemistry reaction chamber module.

Large-scale sequencing of DNA may be performed with the use of dense andhighly parallel sequencers. Sequencing units may be aggregated ontolarge wafers that are placed into chambers for DNA delivery to thesequencing units. The same synthesis module may be used, but this timefor sequencing, and is referred to as a sequencing module. Thesequencing module may or may not use centrifugal forces andvacuum/pressure to add or evacuate reagents from the chamber. Thesequencing module may be light-based (with light sources and sensors onchip), nanopore-based (like Oxford Nanopore Technologies (ONT)), orinvolve other operations (e.g., a light-based method such as PacBio orother sequencing technologies).

A DNA manufacturing, storage, and access system 100 is shown in a blockpictorial flow diagram in FIG. 1A. System 100 may be used to massproduce, store, and access DNA encoded with data to provide anend-to-end solution. System 100 is first described at a high processflow level, with details of the components and processes described infurther detail with respect to further figures.

A synthesis unit or module 110 receives a digital representation of DNAsequences 105, such as one or more polynucleotide sequences that encodedata to be stored. In various embodiments, the sequences may be encodedwith redundancy and various pairs of primers (ID sequences) to allow alevel of random access of the data. One or more wafers may be rotatablymounted within a synthesis unit chamber 115, and fluids provided andevacuated from one or more ports. Synthesis of the DNA identified by thedigital representation of DNA sequences 105 is performed by injectingfluids and draining them from the chamber 115 in succession. Rotation ofthe wafers may assist with fluid evacuation. The DNA is deprotected andcleaved by filling the chamber 115 with cleavage/deprotection reagentsand heating up the chamber 115 for a few hours. Cleaving can occur in arange of pressures from 0-100 psi at varying temperatures and times.

A flexible chemistry reaction chamber module 120 receives fluids fromthe synthesis module 110, such as by fluidic piping 125, and processesthe DNA. Processing the DNA may include amplifying the DNA for eitherstorage, or sequencing and checking to ensure the information wascorrectly encoded. The fluid may comprise a solvent containing thesynthesized DNA. The flexible chemistry reaction chamber module 120filters the fluids using filters designed to ensure the DNA sticks tothe filters, while solvent flows to recycling or waste. The DNA may thenbe eluted into a flexible chemistry reaction chamber where additionalreagents for the PCR or other processing may be added. The chamber maybe alternately heated and cooled to thermocycle the DNA and reagents.

Once the flexible chemistry reaction chamber module 120 completesprocessing of the DNA, the DNA may be cleaned up by a similar filter.The cleaned DNA may be provided via fluidics to a storage platedeposition unit, or encapsulation unit 130, and the DNA is deposited in20 different wells (or a different arbitrary number) of a high-densityphysical storage plate 140, along with other materials to preserve theDNA in capsules for long-term physical storage.

The physical storage plate 140 may be moved into a physical storagearray/library 150 via a robot picker, or a person, for example. Thestorage array/library 150 may contain many such storage plates, and maymaintain an environment suitable for storage of DNA. The capsules may bedried for long-term storage via evaporation or baking at a temperatureat which the DNA will not be damaged. Such drying may occur prior toplacement of the plate 140 into the storage array/library 150, in someembodiments. Lowering the pressure below atmospheric pressure will alsoassist with evaporation. Low temperatures will reduce DNA degradation.In further embodiments, elevated temperatures may optionally be used toincrease rate of evaporation. Lyophilization/freeze-drying may also beused.

To retrieve the DNA, storage plate 140 is retrieved from the storagearray/library 150, and one (or more) of the capsules is “pressed-out” ofthe physical storage plate by a plunger 155. The pressed-out capsule maybe placed in a chamber of a retrieval/hydration unit 160 where newfluids are added, agitated, and optionally heated to dissolve thechemicals used for preservation and rehydrate the DNA. The use of warmedfluids may also help rehydrate, resuspend, and/or re-dissolve the DNA.Unit 160 may be similar in construction to flexible chemistry reactionchamber module 120, and may have an additional valve to seal a chamberfor rehydration. In addition, unit 160 does not include filter materialto allow the capsules to enter a rehydration chamber unimpeded.

Next, the retrieved DNA is filtered and may optionally go through PCR(using the same process as before) in a second flexible chemistryreaction chamber module 170, which may be identical to flexiblechemistry reaction chamber module 120 in some embodiments. In someembodiments, the retrieved DNA may be able to be sequenced and readwithout the need for further PCR. Additional sequencing preparationsteps can be performed in the flexible chemistry reaction chamber module120 or a series of such modules if necessary such as by using magnets orelectromagnets associated with the flexible chemistry reaction chambermodule 120.

Finally, the DNA is moved into a sequencing unit 180, and a voltage maybe applied to draw the DNA through nanopores, which read the data. Othermethods of sequencing may be used in further embodiments. The sequencingunit 180 may have the same or similar construction as the synthesismodule 110.

In various embodiments, the above components may be coupled via one ormore tubes for transferring the DNA in various forms between thecomponents, as well as one or more robots for transferring the storageplates 140 between components as well as controlling the plunger 155 toremove capsules from the plates 140 into chambers of one or morecomponents. Robots may also be used to transfer the DNA using pipettesor test tubes. Various tubes and other components that come in contactwith the DNA may be made of materials to which DNA does not easilyadhere, unless adherence is desired. Example materials that may be usedto form the tubes include polypropylene. Kapton, and EPDM (ethylenepropylene diene monomer) coated materials. Note that other elements maybe designed such that DNA does adhere, such as various filters and otherelements used to retain DNA while flushing fluids from components.

The synthesis module 110 then manufactures the specified digitalrepresentation of DNA sequences 105. When synthesis is complete, thesynthesis module 110 deprotects, cleaves, and elutes the DNA from thewafer surface. A robot or fluidic tube transports the DNA in solution tothe chamber in the flexible chemistry reaction chamber module 120 forsize selection and PCR or other type of amplification or preparation forstorage. In the process of producing DNA of a certain length, say 150nucleotides, shorter or longer strands may also be produced due toinefficiencies in the process. Size selection involves selecting DNA inthe target size and rejecting strands that are much shorter or muchlonger. This process is referred to as size selection. In someimplementations, filters may be tuned to capture DNA of a particularsize range. Other methods include PCR, electrophoresis, and capture bysolid phase bound primers, which are complementary to the end sequencesof synthesized oligonucleotides.

Once prepared, the DNA is moved, again via robot or tube, to theencapsulation unit 130, storage, retrieval and recovery system, and theDNA synthesized in one pool is stored, preserved, and sealed in one ormore wells of one or more plates 140. The one or more plates 140 maythen be stored in slots or drawers of one or more of storagearray/library 150. A DNA pool can also be added to existing, partiallyfilled well or cavities in one or more plates. In further embodiments,the DNA may be stored on a surface of the one or more plates 140. Wells,if used, may be cylindrical wells, or any other shape, having a desiredcross section and/or depth.

When data is requested, the file system and controller 181 determineswhere the physical DNA can be found. The plate 140 is retrieved by arobotic system and the DNA is pushed out of its enclosure in a well andrecovered. The recovered DNA may be added to another flexible chemistryreaction chamber module 160, which may operate as a retrieval/hydrationunit where the DNA is separated from chemicals it may be preserved in.Next, it may be amplified, size selected, randomly accessed via a secondflexible chemistry reaction chamber module 170, ligated, prepared forsequencing, etc. Finally, it is moved by a robot or tube to thesequencing unit 180, which then returns the electronic representation ofthe sequenced DNA to the file system and controller 181 as representedby line 178. The file system and controller 181 then invokes a decoder,which performs reassembly, error correction, and recovers the requestedbits.

FIG. 1B is a block diagram illustrating the components of FIG. 1A,showing their connections via fluidics and robotic mechanisms fortransferring DNA between the components generally at 183. Referencenumbers for pictorial representations of the components in FIG. 1A arealso used for the same block representations in FIG. 1B. File system andcontroller 181 is shown with a line 178 representing a communicationconnection for transferring control commands to multiple components forsynchronizing and controlling the components to process and transfer DNAvia fluidics, also represented as lines 125, 186, 187, 188, and 189. Thelines representing fluidics also represent suitable valves operatingunder control of file system and controller 181. A pressure module 192is also controlled by file system and controller 181 to provide pressurevariations to the synthesis module 110 and sequencing unit 180. A fluidsource 194 is controlled by file system and controller 181 to providefluids to multiple of the components via additional fluidics that arenot shown for ease of illustration. Note that the fluidic connections inillustrations of the individual components show where the fluid source194 is coupled to provide such fluids for processing. The pressurecontrol module 192 may also provide pressure to various fluidicconnections to facilitate fluid flow rates and ensure minimization ofresiduals. Peristaltic pumps may be used in further embodiments inaddition to or in place of pressure sources. Other types of pumps may beused in further embodiments, such as syringe pumps for example. Fluidsource 194 may have multiple different compartments for storing themultiple different fluids, and may also include a multiplexing valve toconnect the compartments to the components for delivery of the properfluids at proper times.

A robotic picker 196, such as a robot similar to those used insemiconductor processing to move trays of wafers and chips betweenprocessing devices, is controlled by file system and controller 181 topick and place storage plates 140 between encapsulation unit 130,storage array/library 150, and retrieval/hydration unit 160. The picker196 may include a bar code or QR code reader to verify the proper plateis being transported to precise positions between the components so thatDNA can be added to wells, removed from wells, and the plate itself canbe inserted and retrieved into and from correct slots of the storagearray/library 150.

In one embodiment, the system 100 may be used to implement a method 200as shown in flowchart form in FIG. 2. The method 200 may includecomputer-readable instructions, that when executed, control thecomponents shown in FIGS. 1A and 1B to synthesize, store, and read DNAencoded with data.

When data to be encoded in DNA sequences is received, a data storagefile system and controller 181 determines where the synthesized DNAsequences that encode the data will be physically stored, and controlsrobots, actuators, and fluidic valves for processing, transferring,storing, and retrieving DNA at and between the various components. Thecontroller 181 responds to commands for storing and retrieving data fromthe file system portion of file system and controller 181.

Method 200 begins responsive to data being received at operation 210.The received data may be binary data identifying DNA sequences that areencoded representations of data that is to be stored and retrieved, ormay simply be the binary data that is to be stored. If the received datais simply binary data to be stored, the data is encoded into digitalrepresentations of DNA sequences at operation 210. Error checking and/orcorrection codes may be included in the digital representations of DNAsequences. At operation 215, metadata received with the encoded DNAsequences is processed to determine where to physically store DNAsequences that have been processed for storage, as well as informationto initiate and control the processing of the encoded DNA sequences. Themetadata identifies a logical address or addresses for the data to bestored, and how to access the data by identifying one or more pairs ofprimers.

The encoded digital representations of DNA sequences are loaded intosynthesis module 110 by operations 220, which controls the synthesismodule 110 to synthesize the sequences and cleave the resulting DNA.Operations 220 may include multiple cycles of controlling valves toprovide various processing fluids, such as reagents, spinning of thewafers to remove such fluids, controlling valves to provide fluid andmodify pressures, as well as one or more heating cycles if desired,activating electronic actuators on the wafers and sensing conditionswith on-wafer electronic/mechanical sensors. In one embodiment, a DNAoligonucleotide synthesis starts on the wafer surface, which ispre-functionalized with a linker that contains a protected orunprotected hydroxyl or amino group. The linker may also be cleavablechemically, electrochemically, photolytically, thermally, orenzymatically after the DNA synthesis is completed.

Operations 225 transfer the cleaved DNA to a flexible chemistry reactionchamber module where the DNA is amplified to make many copies of thesynthesized DNA. Hundreds to millions of copies may be made in variousembodiments to provide data redundancy and ensure that the original datacan be retrieved. Inputs to the PCR process are the DNA, enzymes, singlenucleotides and other molecules to fuel the reaction. The reagents arethermocycled and the enzymes use the single nucleotides to make a copyof the DNA that is already there. In an ideal world, the DNA woulddouble every cycle, but reality is not as good. Note that the PCRreagents may be replenished throughout the reaction. Operations 225 mayalso include the control of valves to provide various fluids, controlheating and cooling, and also control actuators to open and close valvesand agitate a processing chamber.

The amplified DNA is then transferred by operation 230 to a depositionunit, which is controlled to deposit the amplified DNA into one or moreselected wells of the storage plate 140 that has an array of wells. Thedeposition unit encapsulates reacted DNA sequences by drying to removemoisture and improve storage life. A separate drying unit may be used infurther embodiments to blow air or other gas across the storage platewells. The encapsulation may be physical, or both physical and chemicalin various embodiments. The DNA may be encapsulated in solution ordehydrated in various embodiments. The moisture content may be as closeto 0% as possible in one embodiment, or at a level proven to lead to along and stable storage life. In another embodiment, one or more plateswith DNA may be protected from UV light. In a further embodiment, theplates 140 may be stored in a refrigerator and/or temperature andhumidity controlled library or other environment.

At operation 235, the storage plate 140 may be moved by a robot into theaddressable storage array/library 150 for long, or short-term storage.At operation 240, responsive to a request to retrieve the data, therobot may be controlled to retrieve a selected storage plate, such asstorage plate 140, and position the storage plate 140 proximate to theretrieval/hydration unit 160. Operation 245 controls a plunger torelease the DNA capsule from the well such that the capsule enters arehydration chamber of the retrieval/hydration unit 160. Operation 245also operates a top valve plate to provide a path for the capsule to therehydration chamber. Various fluids are introduced to the chamber andthe capsule is de-encapsulated/rehydrated as described above to resultin rehydrated sequences of DNA.

At operation 250, the rehydrated DNA sequences are transferred to afurther flexible chemistry reaction chamber module, which is controlledto amplify the rehydrated sequences, again by controlling multiplevalves and actuators to provide fluids as well has heating and cooling,to facilitate the process as described in further detail above. Inaddition, preparation steps of adding more reagents, heating/cooling,shaking, etc., may also be performed. The amplified rehydrated sequencesare then provided to sequencing unit 180 by operation 255 for sequencingand reading of the data-encoded DNA at operation 260. The read sequencesare transferred as binary sequence data to the file system andcontroller 181 for decoding and providing the data responsive to therequest.

The respective file system and controller portions that may be used toimplement method 200 and control the components, robots, and fluidicsfor processing the DNA may be implemented in one or more softwaremodules and may be logically separate or integrated together in a singlemodule in different embodiments. Tables or other types of datastructures may be used to correlate logical addressees with physicalstorage locations of the DNA to facilitate both storage and retrieval,and to identify to the controller portion physical locations where thestored DNA resides to properly control robots for storage and retrieval.Processes may be executed by the controller to control the processing ateach component as well as the transfer of DNA between the components.

In one embodiment, the synthesis module 110 includes multiple wafers,such as shown at wafer 300 in FIG. 3. One example chamber 115 mayinclude 25 wafers 300. The middle of each wafer 300 contains an opening305, sized for mounting on a spindle or otherwise coupling a stack ofwafers 300 directly to a rotating component of a motor or drive devicefor rotating the wafers 300. In one embodiment, the wafers may bemounted in a manner suitable for rotating the wafers up to approximately1000 rotations per minute (rpm) or higher, suitable for usingcentrifugal force to remove fluids from the wafers. The number of rpmsmay be varied depending on the characteristics of the fluids. Fluidswith a higher viscosity may be removed using higher rpms than fluidswith lower viscosity. Fluids may be distributed about the wafers viarotations at lower rpms, such as rpms suitable for distributing fluids.In one embodiment, a medium to high vacuum may be used to ensureintroduced fluids occupy the voids within the chamber.

The wafers may be in the shape of a circle or disk. In one embodiment,the wafers are 1.0 mm thick, with a diameter of 300 mm. Controlelectronics 310 may be supported by the wafer 300 and dispersed in acircular pattern radially spaced from opening 305. The controlelectronics 310 may be positioned between the opening 305 and a circulargasket 315, which may extend around the wafer 300 in a circle or otherdesired shape such that when multiple wafers 300 are stacked, therespective gaskets 315 of each wafer 300 mate and form a seal toinsulate the electronics from the rest of the chamber. The seal via thegaskets 315 prevents processing fluids from reaching the electronics.The gaskets 315 may also serve to hold the wafers 300 in place duringrotation by the rotating component. In one embodiment, the opening 305may be potted by simply filling the opening 305 with epoxy, which alsoserves to bond the wafers 300 in the stack together.

A flex cable or flex circuit 320 may be electrically coupled to thecontrol electronics 310, which may include memory chips, for datatransfer to and from the control electronics 310 from and to circuitryexternal to the wafer 300. In some embodiments the control electronics310 may communicate wirelessly via transceivers built into the controlelectronics 310. Inductive power coupling may be used for powering thecontrol electronics 310, and wireless or optical communication means maybe used depending on desired data transfer rates. Power for the controlelectronics 310 may be provided via the flex cable 320, batteriescoupled to the control electronics 310, or via electromagnetic or motionbased transducers coupled to the control electronics 310, obviating theneed for physical electrical connection.

A plurality of reticles 325 may be dispersed in an efficient patternabout the wafer 300, extending radially from the gasket 315. Thereticles 325 may be positioned on or otherwise supported by the wafer300, such as a silicon wafer in one embodiment, and serve to hold fluidand DNA during synthesis, serving as the processing sites for dataencoded DNA manufacturing. In one embodiment, there are four concentriccircles of reticles 325 extending outward from the gasket 315. Standoffwafer pitch fiducials 330 may be formed between the reticles 325 inconcentric circles about the radial edges of the reticles 325 as shownin FIG. 3. The fiducials 330 may be etched or otherwise formed on or inthe wafer 300, and serve as visual markers for imaging and/or otherwisedetecting positions of the reticles 325 on the wafer 300. In oneembodiment, the fiducials 330 may be used for gap control. With accuratefiducial height, the fiducials 330 may also be used to minimize a gaptolerance between wafers 300 in the stack.

In one embodiment, the reticles 325 may be functionalized with a linkerthat contains a protected or unprotected hydroxyl or amino group to aidin DNA synthesis. Reticles control growth of the DNA sequences via avariety of methods including optical, electrochemical, thermal, ormicrofluidic deposition methods. The input to the synthesis module 110is a digital description of desired DNA sequences, while the output ismolecules with DNA sequences that encode information for storage.

Large-scale DNA manufacturing is challenging due to the level ofautomation and delivery/evacuation of chemical reagents to surfaceswhere the DNA is grown. The stacked assembly of DNA synthesis wafersthat are rotatably mounted and supported aids in centrifuging reagentsout of the space between the wafers. The rotatable stack, coupled withpressure control creation in the chamber, provides for completeevacuation of used reagents and admission and filling of new reagents inthe chamber.

For DNA synthesis, the wafers may be exposed to reagents in series,interspersed with activation of elements on the wafers (light sourcesfor optical control, electrodes for pH-based or thermal based electroniccontrol, and throttles for mechanical control). For DNA synthesis, a UVspectrometer or other method may be used to measure DNA concentration.The reagent delivery and evacuation is challenging for a stack ofwafers.

The stack of wafers in one embodiment are enclosed in the chamber 115. Avacuum may be used to completely fill the chamber 115 with one reagentat a time. First, the chamber is emptied by spinning the wafers andapplying a positive pressure. A vacuum is then created and a valve isopened that lets the selected reagent in, completely filling the emptyspaces in the chamber. Next, if needed, active elements in the wafer areactivated. Finally, pressure is used again to evacuate the reagent fromthe chamber, leaving it ready for the next step/reagent.

Cleavage and deprotection of the DNA may be done in the chamber, eithervia pressurized gas injection, or a solution that is then heated (or acombination thereof). The selection of reagents entering and exiting thechamber is done via a configurable valve system. Multiple synthesismodules 110 having chambers with stacks of wafers may be mounted on arack in one embodiment for mass production. The rack may be located in adata center, using mechanical structures commonly used for mountingconventional computing and data storage resources in rack units havingopenings adapted to support disk drives, processing blades, and othercomputer equipment.

FIG. 4A is a perspective view of a synthesis module unit 400. FIG. 4B isa cut-away perspective view of the synthesis module unit 400 showing achamber 405 in which a stack 410 of 25 rotatably mounted wafers isdisposed. The synthesis module unit 400 has an outer shell 415 that iscoupled to the wafer stack 410 and rotates with the wafer stack 410 andchamber 405 in one embodiment.

A rotary servo drive 420 is coupled to the wafer stack 410 and functionsto rotate the wafer stack 410. The drive 420 may be similar to a diskdrive rotary servo drive, and may be controlled via control electronics310 or external control electronics. An internal dry column 425 providesa dry environment for electronics 310 and the flex cable 320.

Fluid may be provided to the wafer stack via a liquid fill/drain line430. Line 430 in one embodiment extends radially from a dual portliquid/gas rotary swivel 435 that aligns with the line 430 responsive tothe wafers not rotating and being properly aligned with line 430. Line430 opens to the chamber 405 near the periphery of the wafer stack. Theswivel 435 is also static in one embodiment, and contains two-waysolenoid valves 440 that operate to controllably open and close toprovide access to the line 430 via a fluid fill port 442 for addingfluid to the wafers via the fluid fill port 442 and for draining fluidfrom the wafers. Other configurations of line 430 may be used in furtherembodiments that serve to provide and evacuate fluid from the chamber405. Orientation of the chamber 405 may be controlled to facilitatedraining of fluid in some embodiments, in addition to the use ofcentrifugal force. Locating the opening of line 430 proximate theperiphery of the wafers, and/or chamber 405 itself, may serve to betterdrain fluid.

The valves 440 also operate to utilize a gas vacuum/pressure line 445via a fluid purge port 446 to controllably increase and reduce pressurein the chamber 405 in which the wafers rotate. The line 445 in oneembodiment extends from the valves 440 through the dry column 425 andextends radially outward toward the outer edges or periphery of thewafers, opening into chamber 405. Other configurations may be used tocontrol the pressure of gas in chamber 405.

In one embodiment, synthesis electronics 450 control a synthesisprocess, including fluidic controls and rotational controls, as well asother process parameters commonly utilized in DNA synthesis. Thesynthesis electronics 450 may also rotate with the outer shell 415 andwafer stack 410. Synthesis electronics 450 may include controller 181,or be in communication with controller 181. The control functions forsynthesis module unit 400 may also be distributed between the one ormore controllers in various embodiments.

Synthesis may be performed using known processes and in particular byusing synthesis module unit 400. Processing fluids may be added to anddrained from the chamber 405 in succession. To inject fluids in thechamber, a light vacuum may be pulled via line 430 from the fluid purgeport 446, and the fluid admission port 442 coupled to line 430 is openedvia the valves 440. To drain fluids from the chamber 405, positivepressure in the chamber 405 in conjunction with centrifuging the waferstack 410 to drain fluids at the fluid purge port 446. The fluid volumeof the chamber may be on the order of 1 liter, but may varysignificantly depending on the scale of the module unit 400 and gapbetween wafers. The DNA in the reticles 325 of the wafers is deprotectedand cleaved by filling the chamber 405 with cleavage/deprotectionreagents and heating up the chamber 405 for a few hours. The entiresynthesis module unit 400 may be heated (and optionally subjected tohigher than atmospheric pressure) by an external heat source in someembodiments, or by optional heating elements thermally coupled to thechamber 405.

Following synthesis via synthesis module unit 400, the fluids from thesynthesis, referred to as DNA solution, are drained via port 442 andtransported by fluidic structures, such as tubes, to retrieval/hydrationunit 160. A flexible chemistry reaction chamber module 500 is shown infurther detail in FIG. 5.

The fluidic structures from port 442 couple to flexible chemistryreaction chamber module 500 at a tube 510 and provide the DNA solutionto an optional filter 515 layer. The filter 515 layer in one embodimentmay be a glass fiber membrane, an anion exchange filter unit or anothersolid phase extraction filter unit to capture synthesized DNA to apassage 518 of filter material, with solvent, salts and other smallmolecule impurities flowing to recycling or waste. Another buffersolution is used to elute the DNA into a flexible chemistry reactionchamber 520 (whose volume is about 10 milliliters in one embodiment),and additional reagents for the PCR or other processing are added atthis point. Hot liquid may be circulated in a fluidic thermal loop 525around the chamber to thermocycle the DNA and reagents. An optionalheating element 528 may be thermally coupled for effecting rapid changesin DNA fluid temperatures in the flexible chemistry reaction chamber520. Once the PCR or other processing completes, the resulting DNAcontaining fluid may be cleaned up by a filter similar to filter 515.Note that PCR may be used to amplify correct sized DNA.

The flexible chemistry reaction chamber module 500 may include a toplayer 530 that is coupled to tube 510 to receive the DNA solution fromthe synthesis module unit 400. The top layer 530 contains a firstpassage 538 that is aligned with passage 518 of filter material to allowfiltered DNA solution into chamber 520.

A first linear actuator 545 is coupled to a bottom valve layer 550having an exit opening 552. The first linear actuator 545 may be used toprovide a valve function for the chamber 520. As shown, the valve isopen, allowing DNA solution to exit the flexible chemistry reactionchamber module 500 via a fluidic tube 555. The first linear actuator 545may controllably move the bottom valve layer 550 laterally to close thevalve by making sure the exit opening 552 is not overlapping with thechamber 520. The surfaces of each adjacent layer may be polished toprovide a fluid-tight seal when contact is maintained. Mating hardened,flat, polished surfaces of the layers provides for a fluidic seal.Ceramic, carbide, and diamond like coatings may be used to provide suchsurfaces.

A second linear actuator 560 is coupled to a chamber layer 565 disposedbetween the filter 515 layer and the bottom valve layer 550. Theadjacent surfaces of each layer are also hardened, flat, and polished toprovide a liquid seal. Second linear actuator 560 may be used to agitatethe chamber 520 in a manner conducive to mixing reagents used for thePCR reaction. Note that the use of hardened, flat, polished surfacesprovides for low friction lateral movement and also vertical retentiveforce, as it is very difficult to vertically separate hardened polishedsurfaces in contact with each other. Thus, the various layers of theflexible chemistry reaction chamber module 500 stay coupled absent asignificant external vertical force applied to them. In someembodiments, the layers may be disposed or otherwise supported in acontainer that provides some vertical force, as well as a horizontalforce to at least one non-moving layer such that the actuators only moveone layer at a time in a controlled manner, as controlled by theelectronics module, such as electronics 310, or an external electronicsmodule.

The container may provide support for the actuators, which may be usedto support the layers and lock the layers in position when not movingthe respective layers. The actuators 545, 560 have an actuator element,such as rods 570 and 575, that contacts the respective layers andlaterally moves into and out of the actuators 545, 560 as indicated bydouble arrow lines 580, 585. Magnets or electromagnets may be used forDNA manipulation in various embodiments.

Once the PCR completes, the DNA may be cleaned up by a filter similar tofilter 515 layer and passage 518 of filter material. The filtered DNA isdeposited in 20 different wells (or a different arbitrary number) of ahigh-density physical storage plate, along with materials to encapsulatethe DNA for long-term physical storage.

FIGS. 6A, 6B, and 6C are block cross sections of the flexible chemistryreaction chamber module 500 illustrating different positions of layersduring data-encoded DNA processing creating different flexible chemistryreaction chamber module states. FIG. 6A shows flexible chemistryreaction chamber module 500 with the actuators 560 and 545 positioningthe tube 510, flexible chemistry reaction chamber 520, and exit opening552 in-line. In the illustrated state, a fluid passthrough state,elution of the amplified DNA solution out of tube 555 may occur. Atdifferent times, such as between amplifying different DNA, the samestate of the flexible chemistry reaction chamber module 500 may be usedto remove fluids and leftover DNA or other material in preparation foramplifying the next batch of DNA.

FIG. 6B illustrates a state of flexible chemistry reaction chambermodule 500 where the first actuator 545 has moved the bottom valve layersuch that the exit opening 552 is blocked by a polished flat surface ofthe bottom valve layer 550. The direction moved is shown by arrow 610.Such state, referred to as a fluid adding state, may be used to addfluids containing DNA and other reagents or processing fluids as desiredfor amplifying the DNA.

FIG. 6C illustrates the use of the second actuator 560 to agitate orotherwise move the chamber layer transverse to the axis of the flexiblechemistry reaction chamber 520, while maintaining a closed flexiblechemistry reaction chamber 520 as illustrated by arrow 620. The stateillustrated in FIG. 6C may be referred to as a closed, or processingstate. In one embodiment, the range of motion of the chamber layer 565is controlled such that agitation may be performed without overlappingeither the exit opening 552 or the tube 510. While the flexiblechemistry reaction chamber 520 is shown to the left of the opening 552and tube 510, agitation may alternatively be performed with the chamber520 on the right side. Both ends of the flexible chemistry reactionchamber 520 abut polished surfaces of the top layer 530 and bottom valvelayer 550 during such agitation, trapping fluids in the chamber 520 forprocessing. Following amplification, the fluid passthrough state shownin FIG. 6A may be used to elute the DNA solution from the flexiblechemistry reaction chamber 520.

FIG. 7 is a perspective illustration of devices 700 involved indepositing the DNA generally. A tube 710 is used to transport thefiltered DNA into wells 715 of a storage plate 720. The storage plate720 is supported by a filling fixture 725 that supports the plate 720 ina recess 730. The recess 730 has a drain 735 coupled to a drain tube 740for removing excess fluid and DNA.

The filtered DNA is provided via tube 710 to a fill head 745 that ismoved laterally, as indicated by arrows 747, along the storage plate 720to fill the wells 715. A film or membrane may be provided on a side ofthe storage plate 720 opposite the side from being filled via fill head745. The film should be sufficient to protect the resulting capsules ofDNA from moisture and preserve the DNA for long periods of time. Examplematerials for the film may include aluminum, gold, other metals,polymers, silica oxide, inorganic salts and sugars, thin film glass,thin polymers like EPDM, Kapton, polypropylene and other non-porousmaterials suitable for protecting the DNA and also removable foraccessing the DNA. The film in some embodiments may be releasable toallow access to the DNA during later retrieval and rehydration. In someembodiments, no film is needed, as the wells may be sized such thatcapillary action and surface tension will keep fluid in the wells.However, in other embodiments, the films may provide hermetic seals tokeep capsules and inert gas in a sealed environment to minimize DNAdegradation over long periods of time.

The fill head 745 in one embodiment has multiple fill tubes 750 coupledto tube 710 arranged in a line transverse to the direction of lateralmovement of the fill head 745. The multiple fill tubes 750 arepositioned above the wells 715 such that fluid eluted from the filltubes 750 fills selected wells 715. In further embodiments, the filltubes 750 may be positioned close to the wells 715 such that capillaryaction fills the wells 715 regardless of the orientation of the devices700.

The fill head 745 may include one fill tube 750 per column of wells 715,such that one pass of the fill head 745 laterally along the columns mayfill all of the wells 715 in the array of wells. Multiple passes may beperformed in further embodiments to ensure complete or a desired amountof filling. The fill tubes 750 may also include valves to preciselycontrol which wells 715 receive DNA during each pass, such thatdifferent data-encoded DNA may be placed in selectable wells on anindividual basis. The valves may be controlled by one or morecontrollers previously referenced. In one example, one or more columnsmay receive the same data-encoded DNA, while one or more other columnsmay receive different or multiple different sets of data-encoded DNA.Further, rows of wells or even individual wells 715 may be selected fora set of data-encoded DNA. The file system and controller 181 maygenerate an address identifying the physical location of each well 715or sequence of wells containing DNA encoded with selected data, and thencontrol the fill tubes 750 during each pass to fill the identified wells715.

Following filling, the plate 720 may be heated to facilitate drying ofthe DNA solution in the wells 715. In one embodiment, as much moistureas possible may be removed from the resulting capsules of DNA. A filmmay be used to cover the DNA in the wells 715 when dried.

In various embodiments, standard robotic equipment may be used to movethe storage plate 720 into and out of the filling fixture 725, and tomove the fill head 745 as desired laterally across the storage plate 720under control of one or more controllers.

FIG. 8 is a partial perspective representation of storage plate 720showing wells 715 in further detail. A row 810 of 20 wells is indicatedat an end 815 of the storage plate 720. Rows may have more or fewerwells 715 in further embodiments, and the size of a well 715 may alsovary depending on the amount of DNA desired to be stored. End 815 in oneembodiment may include encoded markings, such as a bar code 820. The barcode 820 may be encoded with a unique identifier for the plate 720,which may be scanned to confirm that the plate 720 is the correct plateduring various storage and retrieval operations.

The storage plate 720 may be moved into a slot of physical storagearray/library 900 as illustrated in a perspective representation in FIG.9A. A robot may be used to insert one or more storage plates 720 intoselected slots 905 of the storage library 900. In one embodiment, thestorage library 900 may have multiple slots, and include one or moreflanges 915 or other mechanism or means to couple the storage library900 to an equipment rack. Each slot 905 may have a physical location andlogical address that the file system may use to control the robot toidentify the proper slot 905 for each plate. Note that the slots 905 arearranged as an array on an open side of the storage library 900 toprovide a three-dimensional storage space accessible by the robot fromthe open side. The bar code 820 may alternatively be used to identifythe plate or to confirm that the correct plate was stored in the correctslot. Storage plate 720 is shown proximate a slot of the storage library900 and illustrates either insertion into or retrieval from the storagelibrary 900.

FIG. 9B is a perspective view illustrating a storage plate 720 partiallyinserted into a drawer or slot 925 of a storage library 930 having anarrangement of multiple vertically stacked adjacent slots. Storage plate720 has a transport protrusion 935 coupled to an end of the storageplate 720. The transport protrusion 935 may be shaped to mate with twoopposed robot arm protrusions 940 supported by a moveable robot arm 945.The two opposed robot arm protrusions 940 may be shaped to releasablyengage the transport protrusion 935, allowing the robot arm 945 to movethe storage plate 920 into and out of one of the storage library 930slots.

FIG. 9C is a perspective view of storage plate 720 showing furtherdetail of the transport protrusion 935. In one embodiment, the transportprotrusion 935 is a plate that is coupled on one end to the storageplate 720, optionally tapering for a distance away from the storageplate 720, and then having an enlarged portion on a distal end of thetransport protrusion 935 suitable for engaging with the opposed robotarm protrusions 940. Many different shapes of the mating protrusions maybe used in further embodiments.

On an opposite end of the storage plate 720, a pair of opposingretention protrusions 937 and 938 may be formed. The opposing retentionprotrusions 937 and 938 may be used to engage a retention post 952formed on a back of the storage library 930 as shown in a perspectiveview in FIG. 9D of a back of the storage library 930. The opposingretention protrusions 937, 938 may have a suitable spring constant tosecurely hold the storage plate 920 when fully inserted into the slotwhen the protrusions 937, 938 are engaged with the retention post 952.The spring constant may be small enough to allow release of the storageplate 720 with a force compatible with both the retentive force of therobot arm protrusions 940 to allow insertion and removal of the plates.

The robot arm protrusions 940, shown in further detail in perspectiveview in FIG. 9E, should be formed to provide suitable support for thestorage plate 720 as well as sufficient retentive force to ensure thestorage plate 720 is retained during transport. Robot arm protrusions940 may be formed with distal portions that extend toward each other tomate with the enlarged portions of the transport protrusion 935. Theopposed robot arm protrusions 940 may be formed to releasably engage thestorage plate protrusions 937, 938, such as by use of actuators or piezoelectric materials to control a distance between the opposed robot armprotrusions 940 that mate with the enlarged portion of the transportprotrusion 935.

FIG. 9E is a perspective view showing further detail of a storage plateengagement portion 947 of the robot arm 945. The storage plateengagement portion 947 includes the opposed robot arm protrusions 940sandwiched between two support plates 950 and 955. The support plates950 and 955 help support the storage plate 720 when engaged with therobot arm protrusions 940, limiting vertical movement of the storageplate 720 during transport, insertion into the storage library 930 andpicking and placing in various other equipment used for processing andhandling the storage plates and DNA.

To retrieve the DNA, the physical storage plate 720 is retrieved fromthe library 900. One (or more) of the capsules is pressed out of thephysical storage plate 720 as illustrated in FIG. 10 at 10000. A plunger1010 has a portion 1015 sized to fit in a well and move a capsule 1020of DNA through and out of the well in which it is stored. The plunger1010 may be coupled to or used by the robot picker 196 to remove thecapsule from the well. Retrieval of DNA from spots may be performed byelectrowetting via a microfluidic platform configured to provide fluidto each desired spot.

The capsule 1020 is then provided to a rehydration unit 1100 shown in ablock cross section view in FIG. 11A. Rehydration unit 110X) is verysimilar to flexible chemistry reaction chamber module 500, with theaddition of a third linear actuator 1135 coupled to a top valve layer1130. The top valve layer 1130 has an additional opening 1140 to receivethe capsule 1020 and provide the capsule 1020 to a chamber 1120 wherenew fluids are added and agitated to dissolve the capsule 1020 andrehydrate the DNA.

The fluidic structures couple to rehydration unit 1100 at a tube 1110and provide rehydration solutions to the chamber 1120 containing thecapsule 1020. Hot liquid may be circulated in a fluidic thermal loop1125 around the chamber 1120 to thermocycle the DNA and solutions. Anoptional heating element 1128 may be thermally coupled for effectingrapid changes in DNA fluid temperatures in the chamber 1120. Once therehydration completes, the resulting DNA-containing fluid may cleaned upby a filter (similar to filter layer 1170 as shown in FIG. 11B).

Still referring to FIG. 11A, rehydration unit 1100 may include the topvalve layer 1130 that is coupled to tube 1110 to receive varioussolutions for rehydrating the capsule 1020. The top valve layer 1130 iscoupled to the third linear actuator 1135 that operates to move the topvalve layer 1130 laterally with respect to a chamber layer 1165. Themating surfaces of each may be polished to provide a fluid-tight sealwhen contact is maintained. The top valve layer 1130 contains a firstpassage 1138 that is alignable with the chamber 1120 for receivingrehydration fluids. An additional opening 1140, laterally spaced fromfirst passage 1138, may be controllably positioned via the third linearactuator 1135 to accept the DNA capsule 1020 which may be punched out ofthe well directly above or forced through the opening 1140 by theportion 1015 of the plunger 1010.

A first linear actuator 1145 is coupled to a bottom valve layer 1150having an exit opening 1152. The first linear actuator 1145 may be usedto provide a valve function for the chamber 1120. As shown, the valve isopen, allowing DNA solution to exit the rehydration unit 1100 via afluidic tube 1155. The first linear actuator 1145 may controllably movethe bottom valve layer 1150 laterally to close the valve by making surethe exit opening 1152 is not overlapping with chamber 1120. Again,mating polished surfaces of the layers provides for a fluidic seal.

A second linear actuator 1160 is coupled to a chamber layer 1165disposed between the filter layer 1115 and the bottom valve layer 1150.The adjacent surfaces of each layer are also hardened, flat, andpolished to provide a liquid seal. Second linear actuator 1160 may beused to agitate the chamber 1120 in a manner conducive to facilitating arehydration of the DNA. Note that the use of hardened, flat, polishedsurfaces provides for low-friction lateral movement and also verticalretentive force, as it usually requires significant vertical force toseparate polished surfaces in contact with each other. Thus, the variouslayers of the rehydration unit 1100 stay coupled absent an externalvertical force applied to them. In some embodiment, the layers may bedisposed or otherwise supported in a container that provides somevertical force, as well as a horizontal force to at least one non-movinglayer such that the actuators only move one layer at a time in acontrolled manner, as controlled by the electronics module, such aselectronics 310, or an external electronics module. The container mayprovide support for the actuators, which may be used to support thelayers and lock the layers in position when not moving their respectivelayers.

Next, the retrieved and rehydrated DNA may be filtered and thensubjected to PCR using the same process and equipment as illustrated at500 in FIG. 5, but coupled to receive DNA solution from rehydration unit1100 via suitable fluidics, such as one or more tubes and valves.Additional sequencing preparation steps can be performed in the flexiblechemistry reaction chamber 1120 or a series of such chambers ifnecessary.

FIG. 11B is a semi-transparent perspective view of a combined reactionchamber and rehydration module 1162 with like components labeledconsistently with unit 1100. A filter layer 1170 may be similar tofilter layer 515 in FIG. 5 and is positioned between the top valve layer1130 and the chamber layer 1165. A passage 1112 is disposed through thefilter layer 1170. An additional tube 1175 is provided laterally spacedfrom tube 1110. The third linear actuator 1135 is coupled to move boththe top valve layer 1130 and the filter layer 1170 to provide either afiltered passage to the reaction chamber 1120 or a clear passage or pathto the reaction chamber 1120. Moving the combined tube 1110 and passage1112 to align with the reaction chamber 1120 provides a clear passagefor a capsule 1020 of DNA to the reaction chamber 1120 for rehydrationand/or de-encapsulation. In this mode, the module 1162 acts in a mannersimilar to the rehydration unit 1100. Moving the tube 1175 and filterlayer 1170 to align with the reaction chamber 1120 provides a filteredpath for receiving DNA from other units and performing PCR

Bottom valve layer 1150, actuated via first linear actuator 1145, may beformed of, or include, filter material that may be similar to the filtermaterial in filter layer 1170. In addition to tube 1155, which has aclear passage or path through the layer 1150 as indicated at passage1156, layer 1150 may also include a further tube 1180 laterally spacedfrom the tube 1155 for first filtering the solution and then exitingsolution when aligned with the reaction chamber 1120 via the firstlinear actuator 1145. Module 1162 may also include the heating elementsand other thermal loops to facilitate DNA processing.

In one embodiment, once the DNA is rehydrated or otherwise ready forfurther processing in the reaction chamber 1120, other reagents may beadded through tube 1110 and the valves may be controlled to close thereaction chamber 1120. Various cycles of heat and/or vibration may thenbe applied via the actuators and heating mechanisms depending on thereaction desired. Other reagents may be added with additional cyclesperformed as many times as called for by the selected reaction. Theresulting solution may then be output via a filter.

Filtering of solutions being processed in the reaction chamber 1120 maybe accomplished by first passing the solutions through the filtermaterial such that DNA is captured by the filter. The fluid from thesolution from the chamber 1120 flows through the chamber 1120 and out towaste or recycling containers. A second fluid may be introduced into thechamber 1120 and used to elute the DNA from the filter. The second fluidmay have a volume that is much less than the volume of fluids used forprocessing the DNA. During elution, the chamber 1120 may be closed suchthat the DNA remains in the chamber 1120. The eluted DNA may then beprovided to other units or modules for further processing, such assequencing or storage, via tube 1155.

In one embodiment, module 1162 may also prepare the rehydrated DNA forsequencing. One or more processing steps, such as ligation, may be usedto prepare the DNA for sequencing for some sequencing methods. Module1162 may include fluidics coupled between an output to an input of thereaction chamber 1120 to achieve several ligation or other preparationcycles. The types of cycles may be dependent on subsequent sequencingmethods utilized. In further embodiments, multiple modules 1162 may beserially fluidically coupled to perform such ligation cycles.

The actuators may be controlled to isolate the processing chamber 1120from all inputs and outputs for agitating or otherwise moving thechamber 1120 to mix fluids and DNA. Such isolation may be obtained byany combination of actuator positioning in various embodiments. Infurther embodiments, actuators need not be positioned on a same side ofthe module 1162, and could be positioned on opposite sides or at variousangles from each other while also repositioning the inputs and outputsaccordingly to account for the motions of the layers in differentdirections.

Finally, the DNA is moved into a sequencing module 1200 shown in apartially assembled perspective view of wafer 1205 and explodedperspective view of the sequencing module at 1210 in FIG. 12. Thesequencing module 1200 may be the same as or similar to sequencingmodule or unit 400 shown in FIG. 4. In one embodiment, one or morewafers 1213 (one shown) are clamped in a stack between a top layer 1215having an electronics module 1220, an opening 1225, and a fluid inlettube 1230. The wafer or wafers 1213 are encapsulated within a chamber1235 formed by an open cylindrical structure 1240 that is bolted orclamped with the top layer 1215 and supported within an outer shell1243. A top portion of the outer shell 1243 is omitted for illustrationpurposes. Structure 1240 is supported by a controllable rotatingsupport, not shown.

The wafer 1213 may be the same as wafer 300 in FIG. 3, and may alsoinclude multiple radially arranged reticles 1245, electronics 1250, anda flex circuit 1255 that couples to electronics module 1220. Note thatelectronics module 1220 may serve as a connector between electronics1250 and an external controller. Sequencing module 1200 may also includea fluid exit opening and tube 1260 to facilitate removal of fluids andDNA solution from the sequencing module 1200. In one embodimentsequencing module 1200 may rotate to aid in removing liquid duringvarious steps of the sequencing process.

The reticles 1245 may be used to read the DNA sequences. The output is adigital representation of the information encoded in the DNA sequences.DNA may be attracted to the reticles 1245 by a difference in voltage. Inone embodiment, a voltage may be applied to draw the DNA throughnanopores in the reticles 1245. The nanopores may then be read, with thedata provided to the file system and controller 181. Reading mechanismsmay be nanopore based, optical, electronic or other. In furtherembodiments, other sequencing methods may be used.

FIG. 13 is a block schematic diagram of a computer system 1300 toimplement a controller for controlling components, fluidics, and robotsfor synthesizing, storing, and retrieving data-encoded DNA and forperforming methods and algorithms according to example embodiments. Allcomponents need not be used in various embodiments.

One example computing device in the form of a computer system 1300 mayinclude a processing unit 1302, memory 1303, removable storage 1310, andnon-removable storage 1312. Although the example computing device isillustrated and described as computer system 1300, the computing devicemay be in different forms in different embodiments. For example, thecomputing device may instead be a smartphone, a tablet, smartwatch,smart storage device (SSD), or other computing device including the sameor similar elements as illustrated and described with regard to FIG. 13.Devices, such as smartphones, tablets, and smartwatches, are generallycollectively referred to as mobile devices or user equipment. Stillfurther, system 1300 may be implemented as a cloud-based service or inone or more electronics modules separate from or integrated with thevarious components for processing DNA described herein.

Although the various data storage elements are illustrated as part ofthe computer system 1300, the storage may also or alternatively includecloud-based storage accessible via a network, such as the Internet orserver-based storage. Note also that an SSD may include a processor onwhich the parser my be run, allowing transfer of parsed, filtered datathrough I/O channels between the SSD and main memory.

Memory 1303 may include volatile memory 1314 and non-volatile memory1308. Computer system 1300 may include—or have access to a computingenvironment that includes—a variety of computer-readable media, such asvolatile memory 1314 and non-volatile memory 1308, removable storage1310 and non-removable storage 1312. Computer storage includes randomaccess memory (RAM), read only memory (ROM), erasable programmableread-only memory (EPROM) or electrically erasable programmable read-onlymemory (EEPROM), flash memory or other memory technologies, compact discread-only memory (CD ROM), Digital Versatile Disks (DVD) or otheroptical disk storage, magnetic cassettes, magnetic tape, magnetic diskstorage or other magnetic storage devices, or any other medium capableof storing computer-readable instructions.

Computer system 1300 may include or have access to a computingenvironment that includes input interface 1306, output interface 1304,and a communication interface 1316. Output interface 1304 may include adisplay device, such as a touchscreen, that also may serve as an inputdevice. The input interface 1306 may include one or more of atouchscreen, touchpad, mouse, keyboard, camera, one or moredevice-specific buttons, one or more sensors integrated within orcoupled via wired or wireless data connections to the computer, andother input devices. The computer may operate in a networked environmentusing a communication connection to connect to one or more remotecomputers, such as database servers. The remote computer may include apersonal computer (PC), server, router, network PC, a peer device orother common data flow network switch, or the like. The communicationconnection may include a Local Area Network (LAN), a Wide Area Network(WAN), cellular, Wi-Fi, Bluetooth, or other networks. According to oneembodiment, the various components of computer system 1300 are connectedwith a system bus 1320.

Computer-readable instructions stored on a computer-readable medium areexecutable by the processing unit 1302 of the computer system 1300, suchas a program 1318. The program 1318 in some embodiments comprisessoftware to control the various fluidics, pressure module, flexiblechemistry reaction chamber modules, synthesizing units, sequencingunits, robotics, actuators, and other components used in processing DNAfor storage and retrieval. A hard drive, CD-ROM, and RAM are someexamples of articles including a non-transitory computer-readable mediumsuch as a storage device. The terms “computer-readable medium” and“storage device” do not include carrier waves to the extent carrierwaves are deemed transitory. Storage can also include networked storage,such as a storage area network (SAN). Computer program 1318 may be usedto cause processing unit 1302 to perform one or more methods oralgorithms described herein.

FIG. 14 is a perspective view of a system 1400 for processing aplurality of wafers 1410 held in a wafer boat 1420. The boat 1420 mayinclude features to support the wafers 1410 in a vertical orientationwith spacing between the wafers 1410 to allow exposure to one or moreliquids in one or more dipping bath containers 1430 via a cable 1440coupled to the boat 1420. A wafer boat used for holding semiconductorwafers in common semiconductor processing processes may be used in oneembodiment. System 1400 facilitates processing of wafers to synthesizeDNA utilizing available semiconductor type trays and bath containersfilled with reagents and other fluids used in common DNA processingmethods.

FIG. 15 is a perspective view of a device 1500 for processing one ormore stacks of wafers 1510 supported by one or more trays 1520. Thetrays 1520 may be moved into a chamber 1530 used for processing thewafers 1510. Device 1500 may be used for different processing steps,such as physical or chemical vapor deposition, chemical-mechanicalplanarization, lithography, annealing, and other processes that areperformed by different semiconductor processing devices. One or more ofdifferent types of devices represented by device 1500 may be used in theprocessing of DNA on the wafers 1510, such as steppers for patterning,deposition machines, and others. An input/output device such astouchscreen 1550 may be used to control device 1500. Device 1500 mayalso be controlled via file system and controller 181 in furtherembodiments.

EXAMPLES

In example 1, a system includes a synthesizer unit having a fluid inputto receive fluids and a communication input to receive commands tosynthesize data-encoded DNA sequences and cleave the DNA. A firstflexible chemistry reaction chamber module may be fluidically coupled tothe synthesizer unit to receive the data encoded DNA sequences andamplify the sequences. A deposition unit may be fluidically coupled tothe first flexible chemistry reaction chamber module to receive theamplified DNA sequences and encapsulate the amplified DNA sequences intoone or more wells in a storage plate for storage and retrieval to andfrom a plate storage unit.

Example 2 includes the system of example 1 wherein the encapsulated DNAsequences are dried, and further comprising a rehydration andde-encapsulation unit coupled to receive the dried encapsulated DNA froma well in the storage plate and rehydrate the DNA.

Example 3 includes the system of any of examples 1-2 and furthercomprising a second flexible chemistry reaction chamber module coupledto receive rehydrated DNA from the rehydration and encapsulation unitand amplify DNA sequences.

Example 4 includes the system of example 3 and further comprises asequencing unit coupled to receive amplified DNA sequences from thesecond flexible chemistry reaction chamber module.

Example 5 includes the system of example 4 wherein the sequencing unitsequences the amplified DNA sequences, reads the sequences, and providesa digital output representative of the sequences.

Example 6 includes the system of example 5 and further comprises acontroller coupled to control the rehydration and de-encapsulation unit,second flexible chemistry reaction chamber module, sequencing unit, andfluidics for transferring DNA sequences therebetween.

Example 7 includes the system of any of examples 1-6 wherein thesequencing unit is coupled to provide the controller the digital output,and wherein the controller is configured to decode the digital outputinto the data encoded into the DNA sequences.

Example 8 includes the system of any of examples 1-7 and furthercomprises a storage unit configured to retrievably hold multiple storageplates.

Example 9 includes the system of any of examples 1-8 and furthercomprises a controller coupled to control the synthesizer unit, flexiblechemistry reaction chamber module, and deposition unit and fluidics fortransferring DNA sequences therebetween.

In example 10, a method includes synthesizing data-encoded DNA sequencesand cleaving the DNA sequences via a synthesizer unit having a fluidinput to receive fluids and a communication input to receive commands tosynthesize data-encoded sequences and cleave the DNA, amplifying the DNAsequences via a first flexible chemistry reaction chamber modulefluidically coupled to the synthesizer unit, and receiving the amplifiedDNA sequences and encapsulating the amplified DNA sequences via adeposition unit fluidically coupled to the first flexible chemistryreaction chamber module into one or more wells in a storage plate forstorage and retrieval to and from a plate storage unit.

Example 11 includes the method of example 10 wherein the encapsulatedDNA comprises dried DNA, and further including receiving theencapsulated DNA from a well in the storage plate at a rehydration andde-encapsulation unit and rehydrating and recovering the encapsulatedDNA.

Example 12 includes the method of example 11 and further includesamplifying the rehydrated DNA at a second flexible chemistry reactionchamber module coupled to receive rehydrated DNA from the rehydrationand encapsulation unit and preparing the amplified DNA for sequencing.

Example 13 includes the method of example 12 and further includesreceiving the amplified and prepared DNA from the second flexiblechemistry reaction chamber module at a sequencing unit fluidicallycoupled to the second flexible chemistry reaction chamber module andproviding a digital output representative of the sequences.

Example 14 includes the method of example 13 and further includescontrolling the rehydration and de-encapsulation unit, second flexiblechemistry reaction chamber module, sequencing unit, and fluidics fortransferring DNA sequences therebetween via a computer implementedcontroller.

Example 15 includes the method of example 14 wherein the controller isconfigured to receive the digital output and decode the binary outputinto the data encoded into the DNA sequences.

Example 16 includes the method of any of examples 10-15 and furthercomprises controlling, via a computer-implemented controller, thesynthesizer unit, flexible chemistry reaction chamber module, depositionunit, and fluidics for transferring DNA sequences therebetween.

In example 17, a machine-readable storage device has instructions forexecution by a processor of the machine to perform operations. Theoperations include controlling synthesizing data-encoded DNA sequencesand cleaving the DNA sequences via a synthesizer unit having a fluidinput to receive fluids and a communication input to receive commands tosynthesize data-encoded sequences and cleave the DNA, controllingamplifying the DNA sequences via a first flexible chemistry reactionchamber module fluidically coupled to the synthesizer unit, andcontrolling receiving of the amplified DNA sequences and encapsulatedthe amplified DNA sequences via a deposition unit fluidically coupled tothe first flexible chemistry reaction chamber module into one or morewells in a storage plate for storage and retrieval to and from a platestorage unit.

Example 18 includes the machine-readable storage device of example 17wherein the encapsulated DNA sequences comprise dried DNA sequences, andfurther including controlling receiving the encapsulated DNA from a wellin the storage plate at a rehydration and de-encapsulation unit andcontrolling rehydrating and recovering the encapsulated DNA.

Example 19 includes the machine-readable storage device of example 18and further includes controlling amplifying the rehydrated DNA andpreparing the amplified DNA for sequencing at a second flexiblechemistry reaction chamber module coupled to receive rehydrated DNA fromthe rehydration and encapsulation unit, controlling receiving theamplified DNA from the second flexible chemistry reaction chamber moduleat a sequencing unit fluidically coupled to the second flexiblechemistry reaction chamber module, and controlling providing a digitaloutput representative of the sequences.

Example 20 includes the machine-readable storage device of any ofexamples 17-19 and further comprises controlling the rehydration andde-encapsulation unit, second flexible chemistry reaction chambermodule, sequencing unit, and fluidics for transferring DNA sequencestherebetween via a computer-implemented controller.

Second Set of Examples

In example 1, a system processes DNA sequences. The system includes asynthesis unit having a synthesis chamber with a wafer-shaped substratehaving multiple reticles for synthesizing DNA sequences, the synthesisunit having an input for receiving DNA sequences and processing fluids,and an output for eluting synthesized DNA in a DNA solution, a flexiblechemistry reaction chamber module for processing the DNA sequences, theflexible chemistry reaction chamber module having an input and anoutput, a deposition DNA unit having an input and an output, multipleplates having wells for holding DNA, a storage library having slots forholding plates, a rehydration unit having multiple inputs and an outputto rehydrate DNA, a second flexible chemistry reaction chamber modulefor processing rehydrated DNA sequences, a sequencer unit having asequencing chamber with a wafer-shaped substrate having multiplereticles for sequencing DNA sequences, the sequencer unit having aninput for receiving processed DNA sequences and a digital signal output,a fluidic network coupled to the units for transferring DNA sequencesbetween the units and providing processing fluids to the units, and arobot coupled to transfer plates between units.

Example 2 includes the system of example 1 and further includes acontroller coupled to control the units, fluidics, and robot.

Example 3 includes the system of any of examples 1-2 and furthercomprises a pressure control unit coupled to vary pressure in one ormore of the synthesis unit, flexible chemistry reaction chamber module,rehydration unit, second flexible chemistry reaction chamber module, andsequencer unit.

Example 4 includes the system of example 3 wherein the pressure controlunit decreases pressure to fill chambers and increases pressure toevacuate fluids from the chambers.

Example 5 includes the system of example 3 wherein the fluidic networkis further coupled to the units and modules for transferring DNA betweenthe units and modules.

Example 6 includes the system of any of examples 1-5 wherein the robotis configured to position the plates for deposition of the DNA in thewells, insert and retrieve the plates in selected slots of the storagelibrary, and position plates for inserting DNA from the wells into thedehydration unit.

Example 7 includes the system of any of examples 1-6 wherein the unitsand modules are supported in rack units.

Example 8 includes the system of any of examples 1-7 wherein the secondflexible chemistry reaction chamber comprises recirculating fluidics forpreparing the amplified DNA for sequencing.

Example 9 includes the system of example 8 wherein the recirculatingfluidics facilitate multiple preparation cycles to prepare the amplifiedDNA for sequencing.

Example 10 includes the system of any of examples 1-9 wherein thedeposition DNA unit is operable to encapsulate the DNA by adding otherchemicals to the DNA, depositing the DNA and chemicals in the wells, anddrying the DNA.

Example 11 includes the system of example 10 wherein the deposition DNAunit is further operable to seal the wells holding the DNA toencapsulate the DNA.

Example 12 includes the system of any of examples 10-11 wherein thedeposition DNA unit is further operable to dry the DNA and chemicals inthe wells.

Example 13 includes the system of any of examples 1-12 wherein the robotis coupled to transfer the plates between the deposition DNA unit,storage library slots, and rehydration unit.

In example 14, a computer-implemented method for processing DNAsequences includes controlling a synthesis unit having a synthesischamber with a wafer-shaped substrate having multiple reticles forsynthesizing DNA sequences, to receive DNA sequences and processingfluids, to synthesize the DNA sequences and output the synthesized DNAin a DNA solution, controlling a flexible chemistry reaction chambermodule to receive the synthesized DNA and reagents and process the DNAsequences, controlling a deposition DNA unit to deposit the DNAsequences onto wells of a plate, controlling a robot to place the platesinto slots of a storage library and transferring plates from the storagelibrary to a rehydration unit, controlling the rehydration unit torehydrate DNA, controlling a second flexible chemistry reaction chambermodule to prepare the rehydrated DNA sequences for sequencing, andcontrolling a sequencer unit having a sequencing chamber with awafer-shaped substrate having multiple reticles for sequencing DNAsequences to receive the prepared DNA sequences and provide a digitalsignal output.

Example 15 includes the method of example 14 wherein the deposition DNAunit is operable to encapsulate the DNA by adding other chemicals to theDNA, drying the DNA, and depositing the DNA and chemicals in the wells.

Example 16 includes the method of example 15 wherein the deposition DNAunit is further operable to seal the wells holding the DNA toencapsulate the DNA.

Example 17 includes the method of any of examples 15-16 wherein thedeposition DNA unit is further operable to dry the DNA and chemicals inthe wells.

Example 18 includes the method of any of examples 14-17 and furthercomprises controlling a fluidic network coupled to the units to transferDNA sequences between the units and provide processing fluids to theunits.

Example 19 includes the method of any of examples 14-18 and furthercomprises controlling a pressure control unit coupled to vary pressurein one or more of the synthesis unit, flexible chemistry reactionchamber module, rehydration unit, second flexible chemistry reactionchamber module, and sequencer unit.

Example 20 includes the method of example 19 wherein the pressurecontrol unit is controlled to decrease pressure to fill chambers of themodules and units and increase pressure to evacuate fluids from thechambers.

Example 21 includes the method of any of examples 19-20 wherein thefluidic network is further controlled to transfer DNA between the unitsand modules.

Example 22 includes the method of any of examples 14-21 wherein therobot is controlled to position the plates for deposition of the DNA inthe wells, insert and retrieve the plates in selected slots of thestorage library, and position plates for inserting DNA from the wellsinto the dehydration unit.

Example 23 includes the method of any of examples 14-22 wherein thesecond flexible chemistry reaction chamber is controlled to recirculatefluidics for preparing the amplified DNA for sequencing.

In example 24, a system for processing DNA sequences includes asynthesis unit having inputs for receiving signals representing DNAsequences and processing fluids, and an output for eluting synthesizedDNA in a DNA solution, a first flexible chemistry reaction chambermodule for amplifying the DNA sequences, the first flexible chemistryreaction chamber module having an input and an output a deposition DNAunit having an input and an output multiple plates having wells forholding DNA, a storage library having slots for holding plates,rehydration unit having multiple inputs and an output to rehydrate DNA,a second flexible chemistry reaction chamber module for processingrehydrated DNA sequences, a sequencer unit having an input for receivingprocessed DNA sequences and a digital signal output, a fluidic networkcoupled to the units for transferring DNA sequences between the unitsand providing processing fluids to the units, and a robot coupled totransfer plates between the units.

Example 25 includes the system of example 24 and further comprises acontroller coupled to control the units, fluidics, and robot.

Example 26 includes the system of any of examples 24-25 and furthercomprises a pressure control unit coupled to vary pressure in one ormore of the synthesis unit, first flexible chemistry reaction chambermodule, rehydration unit, second flexible chemistry reaction chambermodule, and sequencer unit, wherein the pressure control unit decreasespressure to fill chambers and increases pressure to evacuate fluids fromthe chambers, and wherein the robot is configured to position the platesfor deposition of the DNA in the wells, insert and retrieve the platesin selected slots of the storage library, and position plates forinserting DNA from the wells into the dehydration unit.

Example 27 includes the system of any of examples 24-26 wherein thesecond flexible chemistry reaction chamber comprises recirculatingfluidics for preparing the amplified DNA for sequencing, whereinrecirculating fluidics facilitates multiple ligation cycles to preparethe amplified DNA for sequencing.

Example 28 includes the system of any of examples 24-26 wherein thefirst flexible chemistry reaction chamber comprises recirculatingfluidics for preparing the amplified DNA for sequencing, whereinrecirculating fluidics facilitates multiple ligation cycles to preparethe amplified DNA for sequencing.

Third Set of Examples

In example 1, a device includes a container forming a cavity, a fluidicinput coupled through the container to the cavity, a fluidic outputcoupled through the container, and a stack of wafers vertically coupledto rotate about an axis supported within the cavity, wherein the wafersinclude one or more reticles to process DNA sequences.

Example 2 includes the device of example 1 wherein the device includes acommunication interface.

Example 3 includes the device of any of examples 1-2 wherein thecommunication interface is operable to receive a digital representationidentifying DNA sequences to synthesize.

Example 4 includes the device of any of examples 1-3 wherein thecommunication interface is operable to transmit a digital representationof data obtained from sequenced DNA.

Example 5 includes the device of any of examples 1-4 wherein thereticles are formed in a pattern extending radially outward on eachwafer.

Example 6 includes the device of example 5 wherein the reticles areformed in concentric circles about a center of each wafer.

Example 7 includes the device of any of examples 5-6 wherein thereticles are separated by one or more fiducials disposed between thereticles.

Example 8 includes the device of any of examples 1-7 and furthercomprises multiple gaskets disposed between the wafers about an inneropening of the wafers.

Example 9 includes the device of any of examples 1-8 wherein the inneropening in combination with the wafers form an internal dry column.

Example 10 includes the device of any of examples 1-9 wherein thefluidic output is positioned proximate a periphery of the cavity.

Example 11 includes the device of any of examples 1-10 wherein thefluidic input is coupled to a pressure source to facilitate evacuationof fluids from the cavity by increasing pressure in the cavity.

Example 12 includes the device of any of examples 1-11 wherein thefluidic output is coupled to a pressure source to facilitate filling ofthe cavity with fluids by decreasing pressure in the cavity.

Example 13 includes the device of any of examples 1-12 and furtherincludes multiple valves coupled to control the flow of fluids in thefluidic input and fluidic output.

Example 14 includes the device of any of examples 1-13 and furthercomprises a motor coupled to controllably rotate the stack of wafers toremove fluid from the wafers for elution via the fluidic output.

Example 15 includes the device of example 14 wherein the motor rotatesthe stack of wafers up to approximately 1000 revolutions per minute.

In example 16, a device includes a container forming a cavity, a fluidicinput coupled through the container to the cavity, a fluidic outputcoupled through the container to elute fluids from the cavity, acommunication connection, and a stack of wafers vertically coupled torotate about an axis supported within the cavity, wherein the wafersinclude one or more reticles to process DNA sequences and wherein thecommunication connection receives data identifying DNA sequences tosynthesize and transmits data representative of sequenced DNA.

In example 17 a method includes receiving fluids in a cavity of acontainer, the fluids being received via a fluidic input coupled throughthe container to the cavity, eluting fluids via a fluidic output coupledthrough the container to the cavity, and rotating a stack of wafersvertically coupled about an axis supported within the cavity, whereinthe wafers include one or more reticles to process DNA sequences.

Example 18 includes the method of example 17 and further comprisesreceiving digital data defining DNA that encodes information to bestored, or transmitting digital data representative of sequencedinformation encoded DNA.

Example 19 includes the method of any of examples 17-18 and furthercomprises increasing pressure in the cavity while rotating the stack ofwafers to elute fluid through the output port positioned proximate aperiphery of the wafers.

Example 20 includes the method of any of examples 17-19 and furtherincludes controlling fluidic valves to selectively provide DNAprocessing fluids to the cavity via the fluidic input and selectivelyelute DNA from the cavity via the fluidic output.

Fourth Set of Examples

In example 1, a device includes a plurality of round wafers coaxiallymounted in a stack and a plurality of DNA processing reticles disposedabout the wafers to process DNA sequences, wherein the wafers arerotatably coupled about a central axis of the wafers to remove DNAprocessing fluids from the wafers in response to rotation of the wafers.

Example 2 includes the device of example 1 wherein the wafers have acentral opening, the device further comprising a gasket disposed betweenadjacent wafers about the central opening.

Example 3 includes the device of example 2 wherein the gasket iscircular in shape and provides a seal between the adjacent wafers.

Example 4 includes the device of any of examples 2-3 wherein thereticles are arranged in a pattern extending radially from the gasket.

Example 5 includes the device of example 4 wherein the reticles areprocessing sites to hold fluid during DNA processing.

Example 6 includes the device of example 4 wherein the reticles are asame size and are arranged in concentric circles of reticles about thecentral opening.

Example 7 includes the device of any of examples 2-6 and furthercomprises a plurality of standoff wafer pitch fiducials formed betweenthe reticles.

Example 8 includes the device of any of examples 2-7 and furthercomprises electronic modules supported on the wafers between the inneropening and gasket and a flex circuit coupled to the electronic modules.

Example 9 includes the device of any of examples 1-8 wherein thereticles further comprise nanopores through which DNA is drawn inresponse to an applied voltage.

Example 10 includes the device of any of examples 1-9 wherein thereticles are functionalized.

Example 11 includes the device of any of examples 1-10 wherein thewafers are formed of silicon.

Example 12 includes the device of any of examples 1-8 wherein thereticles are configured to manipulate the DNA.

In example 13, a device includes a wafer, a plurality of DNA sequencingreticles disposed about the wafer to process DNA sequences, wherein thewafer is rotatable about a central axis of the wafer to remove DNAprocessing fluids from the wafers in response to rotation of the wafer.

Example 14 includes the device of example 13 wherein the wafer has acentral opening.

Example 15 includes the device of example 14 wherein the reticles arearranged in a pattern extending radially from the central opening.

Example 16 includes the device of example 15 wherein the reticles areprocessing sites to hold fluid during DNA processing.

Example 17 includes the device of example 16 wherein the reticles are asame size and are arranged in concentric circles of reticles about thecentral opening.

Example 18 includes the device of any of examples 14-17 and furthercomprises a plurality of standoff wafer pitch fiducials formed betweenthe reticles.

Example 19 includes the device of any of examples 12-18 and furtherincludes electronic modules supported on the wafers between the inneropening and reticles and a flex circuit coupled to the electronicmodules.

Example 20 includes the device of any of examples 14-19 wherein thereticles are functionalized.

In example 21, a method includes exposing a plurality of round waferscoaxially mounted in a stack to a DNA processing fluid to process DNAsequences on a plurality of DNA processing reticles disposed about thewafers and rotating the stack of wafers about a central axis of thewafers to remove the DNA processing fluid from the wafers.

Fifth Set of Examples

In example 1, a DNA processing module includes a DNA processing chamberlayer having a DNA processing chamber disposed therein, a top layerhaving a first input alignable with the DNA processing chamber, a bottomvalve layer having a first output alignable with the DNA processingchamber, a first actuator coupled to move the DNA processing chamberlayer laterally between the top layer and the bottom valve layer, and asecond actuator coupled to move the bottom valve layer to selectivelyseal and elute DNA from the DNA processing chamber.

Example 2 includes the DNA processing module of example 1 and furthercomprises a filter layer coupled to the top layer and disposed betweenthe top layer and the chamber layer.

Example 3 includes the DNA processing module of example 2 and furthercomprises a second input laterally spaced from the first input in thetop layer, wherein the filter layer comprises a passage aligned with thefirst input and a filter material between the second input and theprocessing chamber.

Example 4 includes the DNA processing module of example 3 and furthercomprises a third actuator coupled to the top layer and filter layer toselectably align the first and second inputs with the processingchamber.

Example 5 includes the DNA processing module of any of examples 1-4wherein adjacent layers comprise polished hardened surfaces to formlaterally movable seals between the layers.

Example 6 includes the DNA processing module of any of examples 1-5 andfurther comprising a thermal fluid circulation loop thermally coupled tothe processing chamber.

Example 7 includes the DNA processing module of any of examples 1-6 andfurther comprises a second, filtered output in the bottom valve layer,wherein the second actuator moves the bottom valve layer to provide afiltered or unfiltered output.

Example 8 includes the DNA processing module of any of examples 1-7 andfurther comprises a heating element thermally coupled to the processingchamber in the chamber layer.

Example 9 includes the DNA processing module of any of examples 1-8wherein the first actuator is operable to agitate the processingchamber.

Example 10 includes the DNA processing module of any of examples 1-9wherein at least one of the outputs is fluidically coupled to at leastone of the inputs to prepare DNA for sequencing.

In example 11, a DNA processing module includes a DNA processing chamberlayer having a DNA processing chamber disposed therein, a top layerhaving a first input and a second input alignable with the DNAprocessing chamber, a bottom valve layer having a first output and asecond output alignable with the DNA processing chamber, a firstactuator coupled to move the DNA processing chamber layer laterallybetween the top layer and the bottom valve layer, a second actuatorcoupled to move the bottom valve layer to selectively seal and elute DNAfrom the DNA processing chamber, and a third actuator coupled tolaterally move the top layer.

Example 12 includes the DNA processing module of example 11 and furthercomprises a filter layer coupled to the top layer and disposed betweenthe top layer and the chamber layer.

Example 13 includes the DNA processing module of example 12 wherein thesecond input is laterally spaced from the first input in the top layerand wherein the filter layer comprises a passage aligned with the firstinput and a filter material between the second input and the processingchamber.

Example 14 includes the DNA processing module of example 13 wherein thethird actuator is coupled to the top layer and filter layer toselectably align the first and second inputs with the processingchamber.

Example 15 includes the DNA processing module of any of examples 11-14wherein adjacent layers comprise polished hardened surfaces to formlaterally movable seals between the layers.

Example 16 includes the DNA processing module of any of examples 11-15and further comprises a thermal fluid circulation loop thermally coupledto the processing chamber.

Example 17 includes the DNA processing module of any of examples 11-16and further comprises a heating element thermally coupled to theprocessing chamber in the chamber layer.

In example 18, a method includes receiving fluid through a first inputin a top layer of a DNA processing module, moving the received fluidinto a processing chamber in a processing chamber layer adjacent to thetop layer, isolating the processing chamber from the first input and afirst output in a bottom valve layer adjacent to the processing chamberlayer to process DNA with the fluid, and eluting fluid and DNA from thefirst output of the bottom valve layer.

Example 19 includes the method of example 18 wherein the adjacent layerscomprise polished hardened surfaces to form laterally moveable seals,and wherein adjacent layers are moved by first and second actuatorscoupled to the processing chamber layer and bottom valve layersrespectively.

Example 20 includes the method of any of examples 18-19 and furthercomprises laterally moving the top layer to selectively align the firstinput and a second, filtered input with the processing chamber via athird actuator.

In example 21, a method includes capturing DNA in a filter as a firstfluid with DNA in a processing chamber of a DNA processing module passesthrough the filter, eluting DNA from the filter with a second fluid inthe processing chamber, and removing the second fluid and DNA from theprocessing chamber.

Example 22 includes the method of example 21 wherein the second fluidvolume is less than the first fluid volume.

In example 23, a method includes adding reagents through a first passagein a processing chamber of a DNA processing module, the processingchamber having DNA therein, closing the processing chamber, processingthe DNA in the reagents, repeating the adding, closing, and processingelements a selected number of times, and removing the reagents and DNAfrom the processing chamber via a second passage.

Sixth Set of Examples

In example 1, a DNA storage device includes a plate having a depth, alength, and a width, an array of wells formed on the plate, wherein thewells are shaped to hold DNA sequences, and a storage library having aplurality of robotically addressable slots, the slots sized toaccommodate the depth, length, and width of the plate.

Example 2 includes the DNA storage device of example 1 wherein the wellsextend through the depth of the plate.

Example 3 includes the DNA storage device of example 2 and furthercomprising a first membrane on a first side of the plate to hold DNAwithin one or more wells.

Example 4 includes the DNA storage device of example 3 and furthercomprising a second membrane on a second side of the plate such that DNAis held within one or more wells between the first and second membranes.

Example 5 includes the DNA storage device of example 4 wherein the DNAsequences are in solution between the first and second membranes.

Example 6 includes the DNA storage device of example 4 wherein the DNAsequences are dehydrated.

Example 7 includes the DNA storage device of any of examples 1-6 whereinthe plate includes a visual code on an end of the plate visible whilethe plate is in a slot of the storage library, the visual code uniquelyidentifying the plate.

Example 8 includes the DNA storage device of any of examples 1-7 andfurther comprises a transport protrusion coupled to a first end of theplate.

Example 9 includes the DNA storage device of example 8 and furthercomprises a pair of opposing retention protrusions coupled to a secondend of the plate, the retention protrusions formed to releasably coupleto a retention post when the plate is fully inserted into a slot.

Example 10 includes the DNA storage device of any of examples 1-9wherein the storage library slots each have a physical location andcorresponding logical address.

Example 11 includes the DNA storage device of any of examples 1-10wherein the storage library comprises one or more flanges for attachingthe storage library to an equipment rack.

In example 12, a DNA storage device includes a plate having a depth, alength, and a width, an array of wells formed on the plate, wherein thewells are shaped to hold DNA sequences, and a transport protrusioncoupled to a first end of the plate for use by a robot to transport theplate to and from a storage library having a plurality of roboticallyaddressable slots, the slots sized to accommodate the depth, length, andwidth of the plate.

Example 13 includes the DNA storage device of example 12 wherein thewells extend through the depth of the plate.

Example 14 includes the DNA storage device of example 13 and furthercomprises a first membrane on a first side of the plate to hold DNAwithin one or more wells.

Example 15 includes the DNA storage device of example 14 and furthercomprises a second membrane on a second side of the plate such that DNAis held within one or more wells between the first and second membranes.

Example 16 includes the DNA storage device of any of examples 12-15wherein the plate includes a visual code on an end of the plate visiblewhile the plate is in a slot of the storage library, the visual codeuniquely identifying the plate.

Example 17 includes the DNA storage device of any of examples 12-16 andfurther comprises a pair of opposing retention protrusions coupled to asecond end of the plate, the retention protrusions formed to releasablycouple to a retention post when the plate is fully inserted into a slot.

Example 18 includes the DNA storage device of any of examples 12-17wherein the storage library slots each have a physical location andcorresponding logical address.

In example 19, a method includes depositing DNA encoded with selecteddata into one or more wells of a plate having a depth, a length, and awidth, the wells formed in an array on the plate, wherein the wells areshaped to hold DNA sequences, and engaging a transport protrusioncoupled to a first end of the plate by a robot to transport the plate toand from a storage library having a plurality of robotically addressableslots, the slots sized to accommodate the depth, length, and width ofthe plate.

Example 20 includes the method of example 19 wherein the wells extendthrough the depth of the plate.

Example 21 includes the method of example 20 and further includesforming a first membrane on a first side of the plate to hold DNA withinone or more wells and forming a second membrane on a second side of theplate such that DNA is held within one or more wells between the firstand second membranes.

Example 22 includes the method of any of examples 19-21 wherein theplate includes a visual code on an end of the plate visible while theplate is in a slot of the storage library, the visual code uniquelyidentifying the plate, the method including reading the visual code toverify that the plate is in a correct slot.

In example 21, a method of using the slide having an array of cavitiesincludes providing metadata, or a pointer thereto, describing datastored in the form of encoded DNA in the cavities, wherein the slideincludes a membrane for allowing removal of fluid while encapsulatingthe DNA in the cavities and optional drying of the DNA, wherein theslide is configured to be inserted in a storage container with otherslides, and removable therefrom for pushing out encapsulated DNA from aselected cavity for de-encapsulation and reading.

Although a few embodiments have been described in detail above, othermodifications are possible. For example, the logic flows depicted in thefigures do not require the particular order shown, or sequential order,to achieve desirable results. Other steps may be provided, or steps maybe eliminated, from the described flows, and other components may beadded to, or removed from, the described systems. Other embodiments maybe within the scope of the following claims.

What is claimed is:
 1. A system comprising: a synthesis unit chambercomprising at least one wafer mounted within the synthesis unit chamberand having a plurality of physically-distinct substrates on the waferfor solid-phase synthesis of DNA, the synthesis unit chamber having afluid input to receive fluids and a fluid output to remove fluids; aPolymerase Chain Reaction (PCR) module fluidically coupled to the fluidoutput of the synthesis unit chamber, the PCR module comprising areaction chamber and a fluidic flow path having an inlet and outlet,wherein the reaction chamber is configured to receive DNA from thesynthesis unit chamber and PCR reagents and the fluidic flow path isconfigured to circulate liquid around the reaction chamber to performPCR amplification of the DNA thereby generating amplified DNA; adeposition unit fluidically coupled to the PCR module to receive theamplified DNA and deposit the amplified DNA into a receptacle; and acontroller communicatively coupled to one or more actuators that openand close valves connected to the synthesis unit chamber, the PCRmodule, and the deposition unit and communicatively coupled to one ormore electronic and/or mechanical sensors that sense conditions on thewafer, wherein the controller is programmed to regulate flow of fluidsbetween the synthesis unit chamber, the PCR module, and the depositionunit by operation of the valves.
 2. The system of claim 1, furthercomprising a rehydration unit configured to receive dried DNA from awell in a storage plate, the rehydration unit comprising a fluid inputto receive rehydration solution and a chamber to maintain therehydration solution in contact with the dried DNA thereby generatingrehydrated DNA.
 3. The system of claim 2, further comprising a secondPCR module fluidically coupled to the rehydration unit and configuredreceive the rehydrated DNA from the rehydration unit, wherein the secondPCR module is configured to perform PCR amplification of the rehydratedDNA thereby generating amplified DNA, the second PCR module comprising areaction chamber and a fluidic thermal loop, wherein the reactionchamber is configured to receive rehydrated DNA from the rehydrationunit and PCR reagents and the fluidic thermal loop is configured tocirculate liquid around the reaction chamber to perform PCRamplification of the rehydrated DNA thereby generating amplified DNA. 4.The system of claim 3, further comprising a sequencing unit fluidicallycoupled to the second PCR module and configured to receive the amplifiedDNA from the second PCR module, wherein the sequencing unit comprises atleast one wafer having one or more nanopores configured to read asequence of DNA deposited on the wafer.
 5. The system of claim 4,wherein the controller is communicatively coupled to the sequencing unitand programmed to decode the sequence of DNA from the sequencing unitinto binary output.
 6. The system of claim 1, further comprising astorage plate holder with multiple slots, a one of the multiple slotsconfigured to retrievably hold a storage plate.
 7. The system of claim1, wherein the at least one wafer is round and mounted within thesynthesis unit chamber.
 8. The system of claim 1, wherein the PCR modulecomprises a linear actuator connected to a rod and configured to agitatethe reaction chamber by moving the rod connected to the reaction chamberlaterally.
 9. The system of claim 7, further comprising a rotary servodrive coupled to the at least one wafer.